VOCAL Tool/Ecosystem
Detector (Script_VOCAL_unified.R)
Rscript --vanilla "vocal/Script_VOCAL_unified.R" \
-v data/ \
-f variants_with_phenotypes.tsv \
-o results/ \
-a meta-information.tsv \
--lineage_column lineage \
--date_column date \
--id_column accession
| Syntax | Description |
|---|---|
| -f | File corresponding to the variants (output from Mutations2Function.py *variants_with_phenotypes.tsv) |
| -a | File containing metadata on the samples |
| -v | Directory path where VOCAL database is stored (files concerned: ECDC_assigned_variants.csv and escape_data_bloom_lab.csv and filiation_information) |
| -o | Output directory |
| -file_annot_latest | File with latest lineage annotation from Desh system [optional argument] |
| --lineage_column | Column name of reporting LINEAGE information in metadata file |
| --date_column | Column name of reporting sampling date information in metadata file |
| --geoloc_column | Column name of geolocalisation information in metadata file |
| --id_column | Column name of the sample ID in metadata file |
Selector tool
'convert-covSonar' command
This tool converts covSonar output (from match command) into VOCAL format.
Required argument;
-i, Input file from covSonar output (*match command)-o, Output file (e.g., variants_with_phenotype_sc2-global.tsv)')-a, Vocal DB, please use "sc2-vocal/data/table_cov2_mutations_annotation.tsv",
Optional argument;
--cpus, Number of cpus to use (default: 1)
Example command;